UC San Diego Researchers Make Strides in Research Reproducibility at Global Biological Standards Meeting

By Tiffany Fox

San Diego, Calif., Oct. 18, 2016 – A University of California San Diego-led effort to improve biomedical research reproducibility continues to gain traction, with experts at the recent Global Biological Standards Institute (GBSI) workshop agreeing to adopt a scoring system based in part on the UC San Diego researchers’ recommendations. The system will help researchers choose reliable antibodies for their experiments and better ensure that research can be replicated.

Anita Bandrowski of the Neuroscience Information Framework is seen here participating in a group discussion about the 3D Virtual Cell project. Bandrowski and her colleagues have developed systems and standards to help researchers select and document biological reagents such as antibodies to better ensure that research can be replicated.

Antibodies are large proteins that are akin to police search dogs – they bind to specific biomolecules, helping researchers track and identify those molecules throughout tissues in the body. But when researchers do not specify in their documentation which antibodies they have used (or they use poorly characterized antibodies), their data is either suspect or not reproducible, which can lead to wasted resources and potential scientific controversy. A scoring and tracking system will both provide a way to validate an antibody’s performance for different kinds of experiments (since not all experiments use antibodies in the same way) and improve researchers’ confidence that a particular antibody will work as expected.

Suggestions for how to develop such a scoring system were published prior to the GBSI workshop in the journal Nature Methods by a team lead by UC San Diego neuroscientist and Qualcomm Institute affiliate Anita Bandrowski. The GBSI organizers aim to spend the next six months drawing on these suggestions for each of the major kinds of experiments that rely on antibodies.

The agreement comes on the heels of announcements by Cell Press and Thermo Fisher Scientific that they will also adopt new labeling and identification standards originally promoted by Bandrowski and her colleagues. Cell Press announced in August that it has redesigned the methodology section in its leading biomedical journal, Cell, to include Structured, Transparent, Accessible Reporting (STAR) Methods. The STAR Methods are designed to label biological reagents (such as specific cell lines, antibodies, chemical agents or types of mice) in a way that makes scientific information flow easier for the author to describe and easier for the reader to replicate. The new methods are designed to align with new reporting guidelines from the National Institutes for Health’s Rigor and Reproducibility Initiative, as well as recommended guidelines from the Resource Identification Initiative, which Bandrowski oversees.

Dorota Skowronska-Krawczyk, an associate project science with the UC San Diego School of Medicine, was one of the first researchers to have a paper published in Cell during the pilot phase of the STAR roll-out.

“These new standards reflect the general need – especially in the Health Sciences – for reproducible data and transparency of the process,” she said. “New standards imposed by publishers are very important, as they may – and should – become just the ‘standard’ procedure in data recording and publishing. I think that the new way of sharing important information about research, once adopted by scientists will not only help to optimally use the limited resources but also will become one of the pillars of faster progress.”

Thermo Fisher Scientific – a San Diego-based multinational biotech company – has also announced it will adopt newly proposed methods (originally proposed by Bandrowski and colleagues in their Nature Methods paper) for validating the antibodies it sells for research applications.

“Labeling and identification standards of research materials promotes transparency and reproducibility of important scientific research,” said Matt Baker, Director of R&D and Business Development, RUO Antibodies at Thermo Fisher Scientific. “We believe the goal of Research Identification Initiative is one very important part of what the International Working Group on Antibody Validation is striving to accomplish – standardized guidelines for antibody specificity, functionality and reproducibility.”